Yes it will. As of January, our testing has shown, this has had a negative impact on the ranking of stores. In fact we sent out an email to all our existing clients telling them that this is harmful for SEO.

I like a tool named Justuno. You can set the pop-up to load after the first page, and/or after a certain amount of time on the site. Google doesn't want you intefering with users getting to your site to see the content they wanted to see. They clicked to see your content/product, not a pop-up.